JP2005537030A5 - - Google Patents
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- JP2005537030A5 JP2005537030A5 JP2004555256A JP2004555256A JP2005537030A5 JP 2005537030 A5 JP2005537030 A5 JP 2005537030A5 JP 2004555256 A JP2004555256 A JP 2004555256A JP 2004555256 A JP2004555256 A JP 2004555256A JP 2005537030 A5 JP2005537030 A5 JP 2005537030A5
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- Prior art keywords
- polynucleotide
- specific marker
- unit specific
- haplotype
- labeled
- Prior art date
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- 238000000034 method Methods 0.000 claims description 59
- 108091033319 polynucleotide Proteins 0.000 claims description 46
- 102000040430 polynucleotide Human genes 0.000 claims description 46
- 239000002157 polynucleotide Substances 0.000 claims description 46
- 239000003550 marker Substances 0.000 claims description 28
- 108091034117 Oligonucleotide Proteins 0.000 claims description 24
- 102000054766 genetic haplotypes Human genes 0.000 claims description 21
- 108020004414 DNA Proteins 0.000 claims description 19
- 239000002773 nucleotide Substances 0.000 claims description 18
- 238000004458 analytical method Methods 0.000 claims description 16
- 238000001514 detection method Methods 0.000 claims description 16
- 239000000523 sample Substances 0.000 claims description 16
- 102000039446 nucleic acids Human genes 0.000 claims description 15
- 108020004707 nucleic acids Proteins 0.000 claims description 15
- 150000007523 nucleic acids Chemical class 0.000 claims description 15
- 125000003729 nucleotide group Chemical group 0.000 claims description 14
- 238000009396 hybridization Methods 0.000 claims description 12
- 238000002372 labelling Methods 0.000 claims description 7
- 108090000623 proteins and genes Proteins 0.000 claims description 7
- 108090000790 Enzymes Proteins 0.000 claims description 6
- 102000004190 Enzymes Human genes 0.000 claims description 6
- 230000000295 complement effect Effects 0.000 claims description 6
- -1 oligo beacon Proteins 0.000 claims description 6
- 230000000694 effects Effects 0.000 claims description 5
- 230000002068 genetic effect Effects 0.000 claims description 4
- 239000001226 triphosphate Substances 0.000 claims description 4
- 235000011178 triphosphate Nutrition 0.000 claims description 4
- 230000005670 electromagnetic radiation Effects 0.000 claims description 3
- 238000009830 intercalation Methods 0.000 claims description 3
- 230000003287 optical effect Effects 0.000 claims description 2
- 238000000137 annealing Methods 0.000 claims 2
- 230000005284 excitation Effects 0.000 claims 2
- 238000012546 transfer Methods 0.000 claims 2
- 108060002716 Exonuclease Proteins 0.000 claims 1
- 108091092878 Microsatellite Proteins 0.000 claims 1
- 108010038807 Oligopeptides Proteins 0.000 claims 1
- 102000015636 Oligopeptides Human genes 0.000 claims 1
- 108091093037 Peptide nucleic acid Proteins 0.000 claims 1
- 108010010677 Phosphodiesterase I Proteins 0.000 claims 1
- 230000009471 action Effects 0.000 claims 1
- 239000003795 chemical substances by application Substances 0.000 claims 1
- 238000004891 communication Methods 0.000 claims 1
- 238000012217 deletion Methods 0.000 claims 1
- 230000037430 deletion Effects 0.000 claims 1
- 201000010099 disease Diseases 0.000 claims 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 claims 1
- 102000013165 exonuclease Human genes 0.000 claims 1
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- 238000003780 insertion Methods 0.000 claims 1
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- 239000002096 quantum dot Substances 0.000 claims 1
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- 230000008707 rearrangement Effects 0.000 claims 1
- 230000003595 spectral effect Effects 0.000 claims 1
- 238000012360 testing method Methods 0.000 claims 1
- 229920000642 polymer Polymers 0.000 description 12
- 238000010586 diagram Methods 0.000 description 9
- ABZLKHKQJHEPAX-UHFFFAOYSA-N tetramethylrhodamine Chemical compound C=12C=CC(N(C)C)=CC2=[O+]C2=CC(N(C)C)=CC=C2C=1C1=CC=CC=C1C([O-])=O ABZLKHKQJHEPAX-UHFFFAOYSA-N 0.000 description 8
- 239000012634 fragment Substances 0.000 description 7
- 230000001419 dependent effect Effects 0.000 description 6
- IQFYYKKMVGJFEH-XLPZGREQSA-N Thymidine Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](CO)[C@@H](O)C1 IQFYYKKMVGJFEH-XLPZGREQSA-N 0.000 description 4
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 4
- 229940088598 enzyme Drugs 0.000 description 4
- 238000003556 assay Methods 0.000 description 3
- SAOKZLXYCUGLFA-UHFFFAOYSA-N bis(2-ethylhexyl) adipate Chemical compound CCCCC(CC)COC(=O)CCCCC(=O)OCC(CC)CCCC SAOKZLXYCUGLFA-UHFFFAOYSA-N 0.000 description 3
- 239000000203 mixture Substances 0.000 description 3
- 239000002090 nanochannel Substances 0.000 description 3
- 239000000126 substance Substances 0.000 description 3
- 108700028369 Alleles Proteins 0.000 description 2
- DWRXFEITVBNRMK-UHFFFAOYSA-N Beta-D-1-Arabinofuranosylthymine Natural products O=C1NC(=O)C(C)=CN1C1C(O)C(O)C(CO)O1 DWRXFEITVBNRMK-UHFFFAOYSA-N 0.000 description 2
- 102000053602 DNA Human genes 0.000 description 2
- 108091028043 Nucleic acid sequence Proteins 0.000 description 2
- IQFYYKKMVGJFEH-UHFFFAOYSA-N beta-L-thymidine Natural products O=C1NC(=O)C(C)=CN1C1OC(CO)C(O)C1 IQFYYKKMVGJFEH-UHFFFAOYSA-N 0.000 description 2
- 239000003086 colorant Substances 0.000 description 2
- 229940104302 cytosine Drugs 0.000 description 2
- HAAZLUGHYHWQIW-KVQBGUIXSA-N dGTP Chemical compound C1=NC=2C(=O)NC(N)=NC=2N1[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 HAAZLUGHYHWQIW-KVQBGUIXSA-N 0.000 description 2
- ZMMJGEGLRURXTF-UHFFFAOYSA-N ethidium bromide Chemical compound [Br-].C12=CC(N)=CC=C2C2=CC=C(N)C=C2[N+](CC)=C1C1=CC=CC=C1 ZMMJGEGLRURXTF-UHFFFAOYSA-N 0.000 description 2
- 229960005542 ethidium bromide Drugs 0.000 description 2
- 102000004169 proteins and genes Human genes 0.000 description 2
- 238000010186 staining Methods 0.000 description 2
- 229940104230 thymidine Drugs 0.000 description 2
- 102000007469 Actins Human genes 0.000 description 1
- 108010085238 Actins Proteins 0.000 description 1
- 102000002260 Alkaline Phosphatase Human genes 0.000 description 1
- 108020004774 Alkaline Phosphatase Proteins 0.000 description 1
- 239000003298 DNA probe Substances 0.000 description 1
- 108010015776 Glucose oxidase Proteins 0.000 description 1
- 239000004366 Glucose oxidase Substances 0.000 description 1
- 108010001336 Horseradish Peroxidase Proteins 0.000 description 1
- 102000003505 Myosin Human genes 0.000 description 1
- 108060008487 Myosin Proteins 0.000 description 1
- 238000012408 PCR amplification Methods 0.000 description 1
- 150000001412 amines Chemical class 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 102000005936 beta-Galactosidase Human genes 0.000 description 1
- 108010005774 beta-Galactosidase Proteins 0.000 description 1
- 125000003178 carboxy group Chemical group [H]OC(*)=O 0.000 description 1
- 238000012790 confirmation Methods 0.000 description 1
- 238000010219 correlation analysis Methods 0.000 description 1
- 238000004925 denaturation Methods 0.000 description 1
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- 238000003745 diagnosis Methods 0.000 description 1
- 239000007850 fluorescent dye Substances 0.000 description 1
- 230000005714 functional activity Effects 0.000 description 1
- 230000014509 gene expression Effects 0.000 description 1
- 229940116332 glucose oxidase Drugs 0.000 description 1
- 235000019420 glucose oxidase Nutrition 0.000 description 1
- 238000003384 imaging method Methods 0.000 description 1
- 239000000138 intercalating agent Substances 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 241000894007 species Species 0.000 description 1
- 125000003396 thiol group Chemical group [H]S* 0.000 description 1
Images
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US37946102P | 2002-05-09 | 2002-05-09 | |
| PCT/US2003/014776 WO2004048514A2 (en) | 2002-05-09 | 2003-05-09 | Methods for analyzing a nucleic acid |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| JP2005537030A JP2005537030A (ja) | 2005-12-08 |
| JP2005537030A5 true JP2005537030A5 (de) | 2006-06-29 |
Family
ID=32393218
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2004555256A Withdrawn JP2005537030A (ja) | 2002-05-09 | 2003-05-09 | 核酸を分析する方法 |
Country Status (5)
| Country | Link |
|---|---|
| US (1) | US20030235854A1 (de) |
| EP (1) | EP1540017A4 (de) |
| JP (1) | JP2005537030A (de) |
| AU (1) | AU2003302463A1 (de) |
| WO (1) | WO2004048514A2 (de) |
Families Citing this family (74)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AU762888B2 (en) | 1997-02-12 | 2003-07-10 | Us Genomics | Methods and products for analyzing polymers |
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| EP1402069A4 (de) * | 2001-06-08 | 2006-01-25 | Us Genomics Inc | Verfahren und produkte zur nukleinsäureanalyse mittels nick-translation |
| EP1546380A4 (de) * | 2002-05-28 | 2007-02-14 | Us Genomics Inc | Verfahren und vorrichtungen mit einzelpolymeranalyse |
| US7282330B2 (en) | 2002-05-28 | 2007-10-16 | U.S. Genomics, Inc. | Methods and apparati using single polymer analysis |
| JP2007501003A (ja) * | 2003-08-01 | 2007-01-25 | ユー．エス． ジェノミクス， インコーポレイテッド | 非切断条件下で核酸を分析するための配列特異的エンドヌクレアーゼの使用に関連した方法および組成物 |
| WO2005017205A2 (en) * | 2003-08-04 | 2005-02-24 | U. S. Genomics, Inc. | Nucleic acid mapping using linear analysis |
| US20050042665A1 (en) * | 2003-08-21 | 2005-02-24 | U.S. Genomics, Inc. | Quantum dots and methods of use thereof |
| WO2005047470A2 (en) * | 2003-11-07 | 2005-05-26 | U.S. Genomics, Inc. | Intercalator fret donors or acceptors |
| JP2007518107A (ja) | 2004-01-13 | 2007-07-05 | ユー．エス． ジェノミクス， インコーポレイテッド | ポリマーを使用する溶液中の分析物の検出および定量化 |
| US7595160B2 (en) | 2004-01-13 | 2009-09-29 | U.S. Genomics, Inc. | Analyte detection using barcoded polymers |
| US7575863B2 (en) * | 2004-05-28 | 2009-08-18 | Applied Biosystems, Llc | Methods, compositions, and kits comprising linker probes for quantifying polynucleotides |
| WO2006017274A2 (en) * | 2004-07-13 | 2006-02-16 | U.S. Genomics, Inc. | Systems and methods for sample modification using fluidic chambers |
| EP1786932A4 (de) * | 2004-08-23 | 2010-10-27 | Us Genomics Inc | Systeme und verfahren zur detektion und analyse von polymeren |
| US7642055B2 (en) * | 2004-09-21 | 2010-01-05 | Applied Biosystems, Llc | Two-color real-time/end-point quantitation of microRNAs (miRNAs) |
| US7262859B2 (en) * | 2004-10-13 | 2007-08-28 | U.S. Genomics, Inc. | Systems and methods for measurement optimization |
| US7888011B2 (en) * | 2004-10-18 | 2011-02-15 | U.S. Genomics, Inc. | Methods for isolation of nucleic acids from prokaryotic spores |
| WO2007011660A2 (en) * | 2005-07-14 | 2007-01-25 | William Marsh Rice University | Quantum dot probes |
| US20070128083A1 (en) * | 2005-07-18 | 2007-06-07 | U.S. Genomics, Inc. | Microfluidic methods and apparatuses for sample preparation and analysis |
| JP4767654B2 (ja) * | 2005-10-21 | 2011-09-07 | 株式会社エヌ・ティ・ティ・ドコモ | 分子伝送・分子配送システムおよび分子伝送・分子配送方法 |
| US20080241071A1 (en) * | 2006-07-14 | 2008-10-02 | West Jennifer L | Quantum Dot Probes |
| WO2008079169A2 (en) | 2006-07-19 | 2008-07-03 | Bionanomatrix, Inc. | Nanonozzle device arrays: their preparation and use for macromolecular analysis |
| EP2092327A2 (de) * | 2006-09-18 | 2009-08-26 | Applied Biosystems, LLC | Verfahren, systeme und vorrichtung für lichtkonzentrationsmechanismus |
| US8999636B2 (en) | 2007-01-08 | 2015-04-07 | Toxic Report Llc | Reaction chamber |
| CA2964611C (en) | 2007-03-28 | 2021-06-01 | Bionano Genomics, Inc. | Methods of macromolecular analysis using nanochannel arrays |
| KR20110025993A (ko) | 2008-06-30 | 2011-03-14 | 바이오나노매트릭스, 인크. | 단일-분자 전체 게놈 분석용 장치 및 방법 |
| US8361716B2 (en) | 2008-10-03 | 2013-01-29 | Pathogenetix, Inc. | Focusing chamber |
| CN108467887A (zh) | 2008-11-18 | 2018-08-31 | 生物纳米基因公司 | 多核苷酸作图和测序 |
| WO2010091024A1 (en) * | 2009-02-03 | 2010-08-12 | Complete Genomics, Inc. | Oligomer sequences mapping |
| WO2010091021A2 (en) * | 2009-02-03 | 2010-08-12 | Complete Genomics, Inc. | Oligomer sequences mapping |
| WO2010091023A2 (en) * | 2009-02-03 | 2010-08-12 | Complete Genomics, Inc. | Indexing a reference sequence for oligomer sequence mapping |
| JP5661251B2 (ja) * | 2009-03-31 | 2015-01-28 | 積水メディカル株式会社 | Ｕｇｔ１ａ１遺伝子多型検出法 |
| EP2430441B1 (de) * | 2009-04-29 | 2018-06-13 | Complete Genomics, Inc. | Verfahren und system zum aufrufen von variationen in einer polynukleotidprobensequenz in bezug auf eine referenzpolynukleotidsequenz |
| US20190300945A1 (en) | 2010-04-05 | 2019-10-03 | Prognosys Biosciences, Inc. | Spatially Encoded Biological Assays |
| US10787701B2 (en) | 2010-04-05 | 2020-09-29 | Prognosys Biosciences, Inc. | Spatially encoded biological assays |
| GB201106254D0 (en) | 2011-04-13 | 2011-05-25 | Frisen Jonas | Method and product |
| US9028776B2 (en) | 2012-04-18 | 2015-05-12 | Toxic Report Llc | Device for stretching a polymer in a fluid sample |
| US8685708B2 (en) | 2012-04-18 | 2014-04-01 | Pathogenetix, Inc. | Device for preparing a sample |
| US8956815B2 (en) | 2012-04-18 | 2015-02-17 | Toxic Report Llc | Intercalation methods and devices |
| EP2909337B1 (de) | 2012-10-17 | 2019-01-09 | Spatial Transcriptomics AB | Verfahren und produkt zur optimierung einer lokalisierten oder räumlichen detektion einer genexpression in einer gewebeprobe |
| LT3013983T (lt) | 2013-06-25 | 2023-05-10 | Prognosys Biosciences, Inc. | Erdviniai koduoti biologiniai tyrimai, naudojant mikrofluidinį įrenginį |
| WO2015027245A1 (en) | 2013-08-23 | 2015-02-26 | Complete Genomics, Inc. | Long fragment de novo assembly using short reads |
| EP4321627A3 (de) | 2015-04-10 | 2024-04-17 | 10x Genomics Sweden AB | Räumlich getrennte multiplex-nukleinsäureanalyse von biologischen proben |
| US20220064630A1 (en) | 2018-12-10 | 2022-03-03 | 10X Genomics, Inc. | Resolving spatial arrays using deconvolution |
| US11649485B2 (en) | 2019-01-06 | 2023-05-16 | 10X Genomics, Inc. | Generating capture probes for spatial analysis |
| US11926867B2 (en) | 2019-01-06 | 2024-03-12 | 10X Genomics, Inc. | Generating capture probes for spatial analysis |
| CN109922430B (zh) * | 2019-03-20 | 2020-12-18 | 苏州真趣信息科技有限公司 | 受限空间作业系统及方法 |
| WO2020243579A1 (en) | 2019-05-30 | 2020-12-03 | 10X Genomics, Inc. | Methods of detecting spatial heterogeneity of a biological sample |
| WO2021092433A2 (en) | 2019-11-08 | 2021-05-14 | 10X Genomics, Inc. | Enhancing specificity of analyte binding |
| US20210190770A1 (en) | 2019-12-23 | 2021-06-24 | 10X Genomics, Inc. | Compositions and methods for using fixed biological samples in partition-based assays |
| ES2982420T3 (es) | 2019-12-23 | 2024-10-16 | 10X Genomics Inc | Métodos para el análisis espacial mediante el uso de la ligazón con plantilla de ARN |
| US11702693B2 (en) | 2020-01-21 | 2023-07-18 | 10X Genomics, Inc. | Methods for printing cells and generating arrays of barcoded cells |
| US11732299B2 (en) | 2020-01-21 | 2023-08-22 | 10X Genomics, Inc. | Spatial assays with perturbed cells |
| US12076701B2 (en) | 2020-01-31 | 2024-09-03 | 10X Genomics, Inc. | Capturing oligonucleotides in spatial transcriptomics |
| US12110541B2 (en) | 2020-02-03 | 2024-10-08 | 10X Genomics, Inc. | Methods for preparing high-resolution spatial arrays |
| US11898205B2 (en) | 2020-02-03 | 2024-02-13 | 10X Genomics, Inc. | Increasing capture efficiency of spatial assays |
| US11732300B2 (en) | 2020-02-05 | 2023-08-22 | 10X Genomics, Inc. | Increasing efficiency of spatial analysis in a biological sample |
| US11891654B2 (en) | 2020-02-24 | 2024-02-06 | 10X Genomics, Inc. | Methods of making gene expression libraries |
| CN115916999A (zh) | 2020-04-22 | 2023-04-04 | 10X基因组学有限公司 | 用于使用靶向rna耗竭进行空间分析的方法 |
| AU2021275906A1 (en) | 2020-05-22 | 2022-12-22 | 10X Genomics, Inc. | Spatial analysis to detect sequence variants |
| EP4153775B1 (de) | 2020-05-22 | 2024-07-24 | 10X Genomics, Inc. | Simultane räumlich-zeitliche messung der genexpression und der zellaktivität |
| US12031177B1 (en) | 2020-06-04 | 2024-07-09 | 10X Genomics, Inc. | Methods of enhancing spatial resolution of transcripts |
| EP4421186A3 (de) | 2020-06-08 | 2024-09-18 | 10X Genomics, Inc. | Verfahren zur bestimmung eines chirurgischen randes und verfahren zur verwendung davon |
| WO2021263111A1 (en) | 2020-06-25 | 2021-12-30 | 10X Genomics, Inc. | Spatial analysis of dna methylation |
| US11761038B1 (en) | 2020-07-06 | 2023-09-19 | 10X Genomics, Inc. | Methods for identifying a location of an RNA in a biological sample |
| US11981960B1 (en) | 2020-07-06 | 2024-05-14 | 10X Genomics, Inc. | Spatial analysis utilizing degradable hydrogels |
| US11981958B1 (en) | 2020-08-20 | 2024-05-14 | 10X Genomics, Inc. | Methods for spatial analysis using DNA capture |
| US11926822B1 (en) | 2020-09-23 | 2024-03-12 | 10X Genomics, Inc. | Three-dimensional spatial analysis |
| US11827935B1 (en) | 2020-11-19 | 2023-11-28 | 10X Genomics, Inc. | Methods for spatial analysis using rolling circle amplification and detection probes |
| EP4121555A1 (de) | 2020-12-21 | 2023-01-25 | 10X Genomics, Inc. | Verfahren, zusammensetzungen und systeme zur erfassung von sonden und/oder barcodes |
| WO2022256503A1 (en) | 2021-06-03 | 2022-12-08 | 10X Genomics, Inc. | Methods, compositions, kits, and systems for enhancing analyte capture for spatial analysis |
| WO2023034489A1 (en) | 2021-09-01 | 2023-03-09 | 10X Genomics, Inc. | Methods, compositions, and kits for blocking a capture probe on a spatial array |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| US4988617A (en) * | 1988-03-25 | 1991-01-29 | California Institute Of Technology | Method of detecting a nucleotide change in nucleic acids |
| US6007987A (en) * | 1993-08-23 | 1999-12-28 | The Trustees Of Boston University | Positional sequencing by hybridization |
| FR2716263B1 (fr) * | 1994-02-11 | 1997-01-17 | Pasteur Institut | Procédé d'alignement de macromolécules par passage d'un ménisque et applications dans un procédé de mise en évidence, séparation et/ou dosage d'une macromolécule dans un échantillon. |
| US20010055812A1 (en) * | 1995-12-05 | 2001-12-27 | Alec Mian | Devices and method for using centripetal acceleration to drive fluid movement in a microfluidics system with on-board informatics |
| AU762888B2 (en) * | 1997-02-12 | 2003-07-10 | Us Genomics | Methods and products for analyzing polymers |
| US6403311B1 (en) * | 1997-02-12 | 2002-06-11 | Us Genomics | Methods of analyzing polymers using ordered label strategies |
| US6210896B1 (en) * | 1998-08-13 | 2001-04-03 | Us Genomics | Molecular motors |
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| US20060008799A1 (en) * | 2000-05-22 | 2006-01-12 | Hong Cai | Rapid haplotyping by single molecule detection |
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| US20050042665A1 (en) * | 2003-08-21 | 2005-02-24 | U.S. Genomics, Inc. | Quantum dots and methods of use thereof |
| WO2005047470A2 (en) * | 2003-11-07 | 2005-05-26 | U.S. Genomics, Inc. | Intercalator fret donors or acceptors |
| JP2007518107A (ja) * | 2004-01-13 | 2007-07-05 | ユー．エス． ジェノミクス， インコーポレイテッド | ポリマーを使用する溶液中の分析物の検出および定量化 |
-
2003
- 2003-05-09 AU AU2003302463A patent/AU2003302463A1/en not_active Abandoned
- 2003-05-09 JP JP2004555256A patent/JP2005537030A/ja not_active Withdrawn
- 2003-05-09 EP EP03811981A patent/EP1540017A4/de not_active Withdrawn
- 2003-05-09 US US10/435,399 patent/US20030235854A1/en not_active Abandoned
- 2003-05-09 WO PCT/US2003/014776 patent/WO2004048514A2/en not_active Application Discontinuation
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